Capture Audio via Digital in Port?

This seems like a basic issue, but I can't find the answer - Is there a way to set my audio capture / input to come in via the Digital in port (TOSLINK, S/PDIF)? I'd like to do this separately from the video capture input. I've found connection information in the FCP documentation, but haven't been able to figure out the settings in the software.
Thanks!

Thanks for the info. So, just to be clear I'll have to run the source twice, once to capture using one of the audio apps and once in FCP to capture the video? I won't be able to capture audio / video at the same time using FCP (audio from the Digital in port and Video from my BlackMagic card)?

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         LineInfo: Master Volume source port
           Port is a SOURCE
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           Controls: 4
         LineInfo: Master Volume target port
           Port is a TARGET
           Controls: 4
         LineInfo: Master Volume target port
           Port is a TARGET
           Controls: 4
         LineInfo: Master Volume target port
           Port is a TARGET
           Controls: 4
         LineInfo: Master Volume target port
           Port is a TARGET
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         LineInfo: interface Clip supporting 8 audio formats, and buffers of at least 32 bytes
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      Target Lines: NONE
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      Controls: NONE
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         LineInfo: interface SourceDataLine supporting 8 audio formats, and buffers of at least 32 bytes
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         LineInfo: interface Clip supporting 8 audio formats, and buffers of at least 32 bytes
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         LineInfo: interface Clip supporting 8 audio formats, and buffers of at least 32 bytes
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           Controls: 2Edited by: user8620608 on Mar 7, 2011 9:51 PM
    Edited by: ags on Mar 8, 2011 9:55 PM
    Shortened code output. Added Exec summary. Trying to make it easy to help.

    It seems that either:
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